Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1q1ra2 | Putidaredoxin reductase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d2naca1 | Formate dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 1.466 --> IntermediateDALI alignment (Z-score: 4.6 Raw score:383.50) query 1 -------------------------------gMENKKMNLLLfsgdydkALASLIIANAA 29 :::::::::: ::::::::::: d1q1ra2 1 rplpvasgavgkannfrylrtledaecirrqlIADNRLVVIG------gGYIGLEVAATA 54 query 30 REMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreAEELPlskmnlggigk 89 :::::::::::: :::: ::::: d1q1ra2 55 IKANMHVTLLDT---AARV------------------------lERVTA----------- 76 query 90 kmllemmkeekapklSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqiMDVKey 147 ::::::::::::::: :::: :::: d1q1ra2 77 -----------ppvsAFYEHLHREAGVDIRtgTQVC---gfemstdqqkvtavlCEDG-- 120 query 148 LKNAleSDLQLFI-- 160 :::: ::::::: d1q1ra2 121 TRLP--ADLVIAGig 133 FAST alignment (Normalized score: 4.48 Raw score:653.70) query 1 -------------------------------GMENKKMNLLLFSGDYDK---ALASLIIA 26 ::::::::: :::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVV---------IGGGYIGLEVA 51 query 27 NAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGG 86 :::::::::::::: d1q1ra2 52 ATAIKANMHVTLLD---------------------------------------------- 65 query 87 IGKKMLLEMMKEEKAP-------------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKE 133 ::::::::::::::::: d1q1ra2 66 ----------------TAARVLERVTAPPVSAFYEHLHREAGVDIR-------------- 95 query 134 ELFPEVQIMDVKEYLKNA----------------------LESDLQLFI---- 160 ::::: ::::::: d1q1ra2 96 ------TGTQV-------CGFEMSTDQQKVTAVLCEDGTRLPADLVI--AGIG 133 TMalign alignment (TM-score: 0.32 Raw score:51.98) query 1 --------------------------------GMENKKMNLLLFSGDYDKALASLIIANA 28 :::::::::::: :::::::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQL---IADNRLVVIGGG-YIGLEVAATAIK 56 query 29 AREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIG 88 :: ::::: ::: :: :::: : : d1q1ra2 57 AN-----MHVTL---LDT-----------------------AA----RVLE---R--V-- 74 query 89 KK--MLL--EMMKEEKAPKLSDLLSGARKKEV-KF--YA----------------XQLSV 125 :: : ::::::::::: : : : ::::: d1q1ra2 75 TAPP--VSA--------FYEHLHREAGV---DI-RTG-TQVCGFEMSTDQQKVTAVLCED 119 query 126 EIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI--- 160 : ::: :: : :::: d1q1ra2 120 G--------------TRL--PA---D-----LVIAGIG 133 HHsearch alignment (Probability: 0.05 E-value:0.02) query 20 LASLIIANAAREMEIEVTIF 39 :::::::::::::::::::: d1q1ra2 45 YIGLEVAATAIKANMHVTLL 64
Intermediate <-- 1.523 --> HitDALI alignment (Z-score: 6.1 Raw score:364.10) d1q1ra2 1 rplpvasgavgkannfrylrtlEDAECIRR--------------------------qlIA 34 :::::::: :: d2naca1 1 -----------------isvaeHVVMMILSlvrnylpshewarkggwniadcvshaydLE 43 d1q1ra2 35 DNRLVVIGGGYIGLEVAATAIKANMHVTLLDtAARVlervtappvSAFYEHLHReagVDI 94 ::::::::::::::::::::::::::::::: :::: ::::::::: ::: d2naca1 44 AMHVGTVAAGRIGLAVLRRLAPFDVHLHYTD-RHRL---------PESVEKELN---LTW 90 d1q1ra2 95 RtgTQVCgfemstdqqkvtavlcedgtrLPADLVIAGIG--------------------- 133 : :::: ::::::::::: d2naca1 91 H--ATRE------------------dmyPVCDVVTLNCPlhpetehmindetlklfkrga 130 d1q1ra2 134 ---------------------------------------------------------- 134 d2naca1 131 yivntargklcdrdavaralesgrlagyagdvwfpqpapkdhpwrtmpyngmtphisg 188 FAST alignment (Normalized score: 4.54 Raw score:718.60) d1q1ra2 1 RPLPVASGAVGKANNFRYLR---TLEDAECIRRQL------------------------- 32 :::::::::: d2naca1 1 --------------------ISVAEHVVMMILS--LVRNYLPSHEWARKGGWNIADCVSH 38 d1q1ra2 33 ---IADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARVLERVTAPPV----SAFYEH 85 ::::::::::::::::::::::::::::::::: :::::: d2naca1 39 AYDLEAMHVGTVAAGRIGLAVLRRLAPFDVHLHYTD--------------RHRLPESVEK 84 d1q1ra2 86 LHREAGVDIRTGTQVCGFEMSTDQQKVTAVLCEDGTR-------LPADLVIAGIG----- 133 : :::::: ::::::::: d2naca1 85 E---LNLTWH---------------------------ATREDMYPVCDVVTLN--CPLHP 112 d1q1ra2 134 ------------------------------------------------------------ 134 d2naca1 113 ETEHMINDETLKLFKRGAYIVNTARGKLCDRDAVARALESGRLAGYAGDVWFPQPAPKDH 172 d1q1ra2 134 ---------------- 134 d2naca1 173 PWRTMPYNGMTPHISG 188 TMalign alignment (TM-score: 0.42 Raw score:56.36) d1q1ra2 1 -------------------------------------------------RPLP-VAS--G 8 :::: ::: : d2naca1 1 ISVAEHVVMMILSLVRNYLPSHEWARKGGWNIADCVSHAYDLEAMHVGTVAAGRIGLAVL 60 d1q1ra2 9 ----------AVG----------------KA-----N---N--F-R-------Y--LRT- 21 ::: :: : : : : : ::: d2naca1 61 RRLAPFDVHLHYTDRHRLPESVEKELNLTWHATREDMYPVCDVVTLNCPLHPETEHMIND 120 d1q1ra2 22 LEDAECIRRQLIADNRLVVI--GGGYIGLEVAATAIKAN-MHVTLLDTAARVLERVTAPP 78 :: :::::: :::::: ::::::::::::::::: :::::::: :::: : d2naca1 121 --ET--LKLFKR--GAYIVNTARGKLCDRDAVARALESGRLAGYAGDV--WFPQ----P- 167 d1q1ra2 79 VSAFYEHLHREAG-VDIRTGTQVCGFEMSTDQQKVTAVLCEDGTRLPADLVIAGIG 133 ::::: :::::: :::::::: : d2naca1 168 APKDH--PWRTMPYNGMTPHIS------------------G--------------- 188 HHsearch alignment (Probability: 0.90 E-value:0.00) d1q1ra2 34 ADNRLVVIGGGYIGLEVAATAIKANMHVTLLDTAARV 70 ::::::::::::::::::::::::::::::::::::: d2naca1 43 EAMHVGTVAAGRIGLAVLRRLAPFDVHLHYTDRHRLP 79